The problems have arisen because of delays in the re-financing of the club by owner Sulaiman al Fahim who completed his protracted takeover in August.
"The club can confirm that the first team squad and Executive Board were not paid yesterday," Portsmouth said in a statement.
"The club is currently being refinanced by the owner Sulaiman al Fahim following the recent completion of his takeover.
"There was a delay in the transfer of funds but the lawyers have received confirmation that this will happen today which will enable the players to be paid within the next 24 to 48 hours. The players have all been informed of the situation."
Last week Al-Fahim said he planned to inject 50 million pounds into the south-coast club over the next month to stabilise its financial position.
The club said the failure to pay the players was a direct consequence of the banks' requirements to retain all television receipts and profits generated during the transfer window in which several high-profile players such as Glen Johnson and Peter Crouch were sold.
In a further statement issued on behalf of directors Peter Storrie, Tanya Robins and Roberto Avondo, they said they supported Al-Fahim's efforts to refinance the club but were very disappointed that contractual obligations to the players had not been met.
"It is clear that in order to ensure that the club is able to its longer term future a more permanent financial solution needs to be found quickly as the executive directors consider it an obligation to the club's loyal employees and fans," the statement said.
News that wages have not been paid is another hammer blow to the club who have lost their opening seven matches of the Premier League season, the worst start by any top-flight team for 79 years.
"I understand the funds have been received and the players will be paid tomorrow (Friday)," manager Paul Hart told the BBC.
"It's one of those glitches that have appeared because of the slowness of the takeover and refunding package. They turned it into a little bit of fun and have been terrific."
While Hart says the players are still in good spirits, it is far from ideal preparation for Saturday's Premier League match at Wolverhampton Wanderers.
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